Human/Swine H1N1 Influenza
Back to Molecular Evolution and Adaptation
Update: 15-July-2009, due to a bug I was considering only the HA gene. Have now updated the analysis to include the HA, NA & M segments.
This is a preliminary survey of sequences submitted to Genbank (09-JUL-2009) by the Canadian Food Inspection Agency isolated from pigs apparently infected with S-OIV in late April, early May. Here are the 8 isolates that have HA, NA and M segments. These sequences seem to have a high number of unique differences compared to the modal sequence. These would give the isolates from this swine herd a large amount of apparent diversity. These mutations may be the result of the passaging history of the isolates before sequencing.
| Isolate | Date of isolation | Number of unique differences to consensus of Alberta swine isolated |
Number of unique differences to consensus of S-OIV isolates as of 30-Jun-2009 |
|---|---|---|---|
| A/swine/Alberta/OTH-33-1/2009 | 3-May-2009 | 6 | 6 |
| A/swine/Alberta/OTH-33-2/2009 | 3-May-2009 | 6 | 6 |
| A/swine/Alberta/OTH-33-3/2009 | 3-May-2009 | 9 | 8 |
| A/swine/Alberta/OTH-33-7/2009 | 5-May-2009 | 12 | 10 |
| A/swine/Alberta/OTH-33-21/2009 | 5-May-2009 | 4 | 4 |
| A/swine/Alberta/OTH-33-23/2009 | 3-May-2009 | 8 | 7 |
| A/swine/Alberta/OTH-33-24/2009 | 3-May-2009 | 7 | 6 |
| A/swine/Alberta/OTH-33-8/2009 | ? | 6 | 6 |
All these sequences are annotated as being passaged in embryonated chicken eggs which have been shown to select for certain mutations. This will produce shared mutations (thus not included in the table above). Passaging in general may introduce random mutations - possibly explaining the unique mutations. We can compare these numbers to those seen in the human S-OIV isolates so far.
Proportion of unique mutations in HA,NA & MA across S-OIV isolates (excluding Alberta swine):
This can be seen in a simple neighbor-joining tree of the sequences (HKY model, arbitrary rooting). This shows that all the Alberta swine sequences cluster together within the human S-OIV but the cluster shows very high diversity.
It seems unlikely that these mutations have arisen due to adaptation for swine transmission after a period of adaptation in humans - we would expect this to bring the same mutations to fixation - we would expect largely identical sequences with a long branch leading to the human hosted viruses.
/groups/influenza/search/index.rss?sort=modifiedDate&sortDirection=reverse&tag=sectionlist/groups/influenza/search/?sort=modifiedDate&sortDirection=reverse&tag=sectionSectionsCustomTagSidebarCustomTagSidebar?sort=modifiedDate&sortDirection=reverse&tag=section0/groups/influenza/sidebar/CustomTagSidebarmodifiedDate5CustomTagSidebarreversesectionSectionscustom/groups/influenza/search/index.rss?tag=hotlist/groups/influenza/search/?tag=hotWhat’s HotHotListHot!?tag=hot20/groups/influenza/sidebar/HotListrambaut2009-07-08 14:53:06+00:002009-07-08 14:53:06updated10Updated links to final versionlycett2009-07-01 05:34:14+00:002009-07-01 05:34:14updated9rambaut2009-06-12 07:40:19+00:002009-06-12 07:40:19updated8Added tag - hotrambaut2009-06-12 07:40:17+00:002009-06-12 07:40:17addTag7rambaut2009-06-12 07:40:08+00:002009-06-12 07:40:08updated6rambaut2009-06-12 07:27:06+00:002009-06-12 07:27:06updated5rambaut2009-06-12 07:17:50+00:002009-06-12 07:17:50updated4rambaut2009-06-12 07:15:25+00:002009-06-12 07:15:25updated3rambaut2009-06-12 07:15:17+00:002009-06-12 07:15:17updated2First additionrambaut2009-06-12 07:13:50+00:002009-06-12 07:13:50created1wiki2009-07-08T14:53:06+00:00groups/influenza/wiki/1b2c3FalseH1N1: Origins and evolution of the current epidemic/groups/influenza/wiki/1b2c3/H1N1_Origins_and_evolution_of_the_current_epidemic.htmlAndrew Rambaut10 updatesH1N1: Origins and evolution of the current epidemic
Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic
Gavin J. D. Smith1, Dhanasekaran Vijaykris...Falserambaut2009-07-08T14:53:06+00:00Shanghai/71T/09 does not have PB2-627Klycett2009-06-28 16:11:04+00:002009-06-28 16:11:04updated7lycett2009-06-28 16:06:53+00:002009-06-28 16:06:53updated6lycett2009-06-19 07:03:23+00:002009-06-19 07:03:23updated5Added tag - hotlycett2009-06-19 07:03:22+00:002009-06-19 07:03:22addTag4A/Shanghai/71T/2009 & PB2-627Klycett2009-06-18 22:40:51+00:002009-06-18 22:40:51updated3PB2-627K on A/Shanghai/71T/2009lycett2009-06-18 22:34:10+00:002009-06-18 22:34:10updated2First additionlycett2009-06-18 22:12:59+00:002009-06-18 22:12:59created1wiki2009-06-28T16:11:04+00:00groups/influenza/wiki/8bc58FalsePB2-627K & PB2-701N in A/Shanghai/71T/2009/groups/influenza/wiki/8bc58/PB2627K__PB2701N_in_AShanghai71T2009.htmlSam Lycett7 updatesPB2-627K & PB2-701N in A/Shanghai/71T/2009
Notes on A/Shanghai/71T/2009
by Sam Lycett
Update 28 June 09
The sequences A/Shanghai/71T/2009 were updated on 24...Falselycett2009-06-28T16:11:04+00:00comas2009-05-10 21:28:29+00:002009-05-10 21:28:29updated6comas2009-05-10 21:27:07+00:002009-05-10 21:27:07updated5comas2009-05-10 21:26:45+00:002009-05-10 21:26:45updated4Added tag - hotcomas2009-05-10 21:26:43+00:002009-05-10 21:26:43addTag3comas2009-05-10 21:26:25+00:002009-05-10 21:26:25updated2First additioncomas2009-05-10 21:13:16+00:002009-05-10 21:13:16created1wiki2009-05-10T21:28:29+00:00groups/influenza/wiki/aba06FalseUpdated Median Joining network (HA genes) - 8 May 2009 - Iñaki Comas/groups/influenza/wiki/aba06/Updated_Median_Joining_network_HA_genes__8_May_2009__Iaki_Comas.htmlIñaki Comas6 updatesUpdated Median Joining network (HA genes) - 8 May 2009 - Iñaki Comas
Here is an update of the median joining network with all swine samples available at GISAID as of 8 of May. The alignment was provided by Oliver Pyb...Falsecomas2009-05-10T21:28:29+00:00pybus2009-05-08 15:45:54+00:002009-05-08 15:45:54updated6pybus2009-05-06 19:32:17+00:002009-05-06 19:32:17updated5Added tag - selectionpybus2009-05-06 18:30:11+00:002009-05-06 18:30:11addTag4Added tag - hotpybus2009-05-06 18:29:59+00:002009-05-06 18:29:59addTag3pybus2009-05-06 18:29:25+00:002009-05-06 18:29:25updated2First additionpybus2009-05-06 18:18:26+00:002009-05-06 18:18:26created1wiki2009-05-08T15:45:54+00:00groups/influenza/wiki/87337FalseAmino acid changes in HA, NA & MP leading to outbreak 6 May 2009 - Oliver Pybus and Samir Bhatt/groups/influenza/wiki/87337/Amino_acid_changes_in_HA_NA__MP_leading_to_outbreak_6_May_2009__Oliver_Pybus_and_Samir_Bhatt.htmlOliver Pybus6 updatesAmino acid changes in HA, NA & MP leading to outbreak 6 May 2009 - Oliver Pybus and Samir Bhatt
So, I hear you ask, what amino acid changes have occurred along those long branches leading to the outbreak strain?
Right, we've gone and ...Falsepybus2009-05-08T15:45:54+00:00comas2009-05-08 12:59:46+00:002009-05-08 12:59:46updated7rambaut2009-05-08 11:40:12+00:002009-05-08 11:40:12updated6Added tag - genetic structurecomas2009-05-08 10:49:11+00:002009-05-08 10:49:11addTag5Added tag - transmissioncomas2009-05-08 10:48:52+00:002009-05-08 10:48:52addTag4comas2009-05-08 10:45:56+00:002009-05-08 10:45:56updated3Added tag - hotcomas2009-05-08 10:44:35+00:002009-05-08 10:44:35addTag2First additioncomas2009-05-08 10:37:39+00:002009-05-08 10:37:39created1wiki2009-05-08T12:59:46+00:00groups/influenza/wiki/8e6d0FalseMedian joining network (HA gene) - 7May2009 - Iñaki Comas/groups/influenza/wiki/8e6d0/Median_joining_network_HA_gene__7May2009__Iaki_Comas.htmlIñaki Comas7 updatesMedian joining network (HA gene) - 7May2009 - Iñaki Comas
I have created a median joining network with the HA sequences present in the NCBI as of 7May2009. This includes 49 isolates from different locat...Falsecomas2009-05-08T12:59:46+00:00hot/groups/influenza/search/index.rss?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomelist/groups/influenza/search/?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcomeRecent ChangesRecentChangesListUpdates?sort=modifiedDate&kind=all&sortDirection=reverse&excludePages=wiki/welcome0/groups/influenza/sidebar/RecentChangesListmodifiedDateallRecent ChangesRecentChangesListUpdateswiki/welcomeNo recent changes.reverse5search
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